7U01 | pdb_00007u01

Structure of CD148 fibronectin type III domain 2

PDB DOI: https://doi.org/10.2210/pdb7U01/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-02-17 Released: 2023-02-22
Deposition Author(s): Zhou, D., Zhu, J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.260 (Depositor), 0.265 (DCC)
R-Value Work:
0.214 (Depositor), 0.217 (DCC)
R-Value Observed:
0.217 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7U01

This is version 1.1 of the entry. See complete history.

Literature

Structure of CD148 fibronectin type III domain 1 and 2

Zhou, D., Zhu, J.

To be published.

Macromolecule Content

Total Structure Weight: 67.83 kDa
Atom Count: 3,267
Modeled Residue Count: 418
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-type tyrosine-protein phosphatase eta	A, B, C, D	159	Homo sapiens	Mutation(s): 0 Gene Names: PTPRJ, DEP1 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q12913 (Homo sapiens) Explore Q12913 Go to UniProtKB: Q12913
PHAROS: Q12913 GTEx: ENSG00000149177
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12913
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.260 (Depositor), 0.265 (DCC)
R-Value Work: 0.214 (Depositor), 0.217 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.068	α = 90
b = 155.068	β = 90
c = 47.837	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
AutoSol	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM137143
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL131836

Revision History (Full details and data files)

Version 1.0: 2023-02-22
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.